Re: [Obo-format] [Go-database] go2fmt help

[chris m. <cj...@fr...>]

Hi Summer

The current conversion is somewhat lossy (you should have the defs  
but not the comments)

This will be fixed in the next release of go-perl. If you want to try  
out the new but not-yet finalised mapping you'll need to get go-dev  
from cvs, then run the following:

  go2fmt.pl -x oboxml_1_2-to-owl gene_ontology.obo > go.owl

The definitions, synonyms, synonym types and so on are preserved.  
However, they may look a little unusual in the native Protege-OWL  
display as Protege doesn't have any built in semantics for the  
annotation properties used to define these. Stuart Aitken (who also  
devised the latest mapping) is developing a Protege-OWL plugin geared  
towards elegant display of the additional terminological information.

Cheers
Chris

On Jun 29, 2006, at 7:09 AM, Summer Hamidian wrote:

> Hello. I hope this is the right mailing list for my question. If it  
> is not, please direct me to where I should be.
>
> I am using go2fmt from the go-perl library to convert OBO files  
> into OWL files. After I do the conversion, I am using Protege to  
> navigate through the terms in the files. The definitions or  
> comments from the OBO files do not seem to appear anywhere in the  
> OWL files. If I use Protege to import an OBO and export an OWL, the  
> definitions appear, but the reason I don't want to use Protege for  
> the conversion is because it doesn't import the OBO the way it should.
>
> Any help is much appreciated.
>
> -Summer
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